Abstract:
Canine atopic dermatitis is a genetically predisposed inflammatory and pruritic allergic skin disease that is often
complicated by (secondary) bacterial and fungal (yeast) infections. High-throughput DNA sequencing was used
to characterize the composition of the microbiome (bacteria and fungi) inhabiting specific sites of skin in healthy
dogs and dogs with atopic dermatitis (AD) before and after topical antimicrobial treatment. Skin microbiome
samples were collected from six healthy control dogs and three dogs spontaneously affected by AD by swabbing
at (non-) predilection sites before, during and after treatment. Bacteria and fungi were profiled by Illumina
sequencing of the 16S ribosomal RNA gene of bacteria (16S) and the internally transcribed spacer of the ribosomal
gene cassette in fungi (ITS). The total cohort of dogs showed a high diversity of microbes on skin with a
strong individual variability of both 16S and ITS profiles. The genera of Staphylococcus and Porphyromonas were
dominantly present both on atopic and healthy skin and across all skin sites studied. In addition, bacterial and
fungal alpha diversity were similar at the different skin sites. The topical antimicrobial treatment increased the
diversity of bacterial and fungal compositions in course of time on both AD and healthy skin.
